Merge pull request #238 from bioperl/fix_indexedbase

Change stray 'wiki/HOW' URLs to new site

Bio/DB/GenericWebAgent.pm

@@ -1,7 +1,7 @@
 #
 # BioPerl module for Bio::DB::GenericWebAgent
 #
-# Please direct questions and support issues to <bioperl-l@bioperl.org> 
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
 #
 # Cared for by Chris Fields <cjfields at bioperl dot org>
 #
@@ -21,7 +21,7 @@ access and response retrieval.
 =head1 SYNOPSIS
 
   # DO NOT USE DIRECTLY
-  
+
   See Bio::DB::EUtilities for an example implementation
 
 =head1 DESCRIPTION
@@ -34,7 +34,7 @@ the user agent (Bio::ParameterBaseI), and a BioPerl class parser that processes
 response content received by the user agent. The Bio::ParameterBaseI object
 should be state-aware, e.g. know when changes occur to parameters, so that
 identical requests are not repeatedly sent to the server (this base class takes
-this into consideration).  
+this into consideration).
 
 =head1 FEEDBACK
 
@@ -47,17 +47,17 @@ of the Bioperl mailing lists. Your participation
 is much appreciated.
 
   bioperl-l@lists.open-bio.org               - General discussion
-  http://www.bioperl.org/wiki/Mailing_lists  - About the mailing lists
+  http://bioperl.org/Support.html  - About the mailing lists
 
-=head2 Support 
+=head2 Support
 
 Please direct usage questions or support issues to the mailing list:
 
 I<bioperl-l@bioperl.org>
 
-rather than to the module maintainer directly. Many experienced and 
-reponsive experts will be able look at the problem and quickly 
-address it. Please include a thorough description of the problem 
+rather than to the module maintainer directly. Many experienced and
+reponsive experts will be able look at the problem and quickly
+address it. Please include a thorough description of the problem
 with code and data examples if at all possible.
 
 =head2 Reporting Bugs
@@ -106,7 +106,7 @@ BEGIN {
  Title   : new
  Usage   : Bio::DB::GenericWebAgent->new(@args);
  Function: Create new Bio::DB::GenericWebAgent instance.
- Returns : 
+ Returns :
  Args    : None specific to this base class.  Inheriting classes will
            likely set specific parameters in their constructor;
            Bio::DB::GenericWebAgent is primarily a test bed.
@@ -173,7 +173,7 @@ sub ua {
  Returns : HTTP::Response object or data if callback is used
  Args    : (optional)
 
-           -cache_response - flag to cache HTTP::Response object; 
+           -cache_response - flag to cache HTTP::Response object;
                              Default is 1 (TRUE, caching ON)
 
            These are passed on to LWP::UserAgent::request() if stipulated
@@ -193,7 +193,7 @@ sub get_Response {
     my ($cache, $file, $cb, $size) = $self->_rearrange([qw(CACHE_RESPONSE FILE CB READ_SIZE_HINT)],@args);
     $self->throw("Can't have both callback and file") if $file && $cb;
     # make -file accept more perl-like write-append type data.
-    $file =~ s{^>}{} if $file; 
+    $file =~ s{^>}{} if $file;
     my @opts = grep {defined $_} ($file || $cb, $size);
     $cache = (defined $cache && $cache == 0) ? 0 : 1;
     my $pobj = $self->parameter_base;
@@ -224,7 +224,7 @@ sub get_Response {
             $cb && ref($cb) eq 'CODE' && $cb->($self->{_response_cache}->content);
         }
         return $self->{_response_cache};
-    }    
+    }
 }
 
 =head2 get_Parser

Bio/DB/LocationI.pm

@@ -1,7 +1,7 @@
 #
 # BioPerl module for Bio::DB::LocationI
 #
-# Please direct questions and support issues to <bioperl-l@bioperl.org> 
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
 #
 # Cared for by Chris Fields <cjfields at bioperl dot org>
 #
@@ -15,7 +15,7 @@
 
 Bio::DB::LocationI - A RandomAccessI-like abstract interface for
 retrieving location data from a sequence database and returning
-Bio::LocationI objects 
+Bio::LocationI objects
 
 =head1 SYNOPSIS
 
@@ -32,7 +32,7 @@ Bio::LocationI objects
 =head1 DESCRIPTION
 
 This is a pure interface class - in other words, all this does is define
-methods which other (concrete) classes will actually implement. 
+methods which other (concrete) classes will actually implement.
 
 The Bio::DB::LocationI class defines methods used to retrieve location data
 from a sequence.  This is returned in the form of Bio::LocationI objects,
@@ -52,24 +52,24 @@ is based.
 
 =head2 Mailing Lists
 
-User feedback is an integral part of the 
+User feedback is an integral part of the
 evolution of this and other Bioperl modules. Send
 your comments and suggestions preferably to one
 of the Bioperl mailing lists. Your participation
 is much appreciated.
 
   bioperl-l@lists.open-bio.org               - General discussion
-  http://www.bioperl.org/wiki/Mailing_lists  - About the mailing lists
+  http://bioperl.org/Support.html  - About the mailing lists
 
-=head2 Support 
+=head2 Support
 
 Please direct usage questions or support issues to the mailing list:
 
 I<bioperl-l@bioperl.org>
 
-rather than to the module maintainer directly. Many experienced and 
-reponsive experts will be able look at the problem and quickly 
-address it. Please include a thorough description of the problem 
+rather than to the module maintainer directly. Many experienced and
+reponsive experts will be able look at the problem and quickly
+address it. Please include a thorough description of the problem
 with code and data examples if at all possible.
 
 =head2 Reporting Bugs
@@ -80,7 +80,7 @@ Bug reports can be submitted via the web.
 
   https://github.com/bioperl/bioperl-live/issues
 
-=head1 AUTHOR 
+=head1 AUTHOR
 
 Email cjfields at bioperl dot org
 

Bio/DB/ReferenceI.pm

@@ -1,7 +1,7 @@
 #
 # BioPerl module for Bio::DB::ReferenceI
 #
-# Please direct questions and support issues to <bioperl-l@bioperl.org> 
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
 #
 # Cared for by Chris Fields <cjfields at bioperl dot org>
 #
@@ -15,7 +15,7 @@
 
 Bio::DB::ReferenceI - A RandomAccessI-like abstract interface for
 retrieving Reference data from a sequence database and returning
-Bio::Annotation::Reference objects 
+Bio::Annotation::Reference objects
 
 =head1 SYNOPSIS
 
@@ -32,7 +32,7 @@ Bio::Annotation::Reference objects
 =head1 DESCRIPTION
 
 This is a pure interface class - in other words, all this does is define
-methods which other (concrete) classes will actually implement. 
+methods which other (concrete) classes will actually implement.
 
 The Bio::DB::ReferenceI class defines methods used to retrieve reference data
 from a sequence.  This is returned in the form of Bio::Annotation::Reference
@@ -48,24 +48,24 @@ is based.
 
 =head2 Mailing Lists
 
-User feedback is an integral part of the 
+User feedback is an integral part of the
 evolution of this and other Bioperl modules. Send
 your comments and suggestions preferably to one
 of the Bioperl mailing lists. Your participation
 is much appreciated.
 
   bioperl-l@lists.open-bio.org               - General discussion
-  http://www.bioperl.org/wiki/Mailing_lists  - About the mailing lists
+  http://bioperl.org/Support.html  - About the mailing lists
 
-=head2 Support 
+=head2 Support
 
 Please direct usage questions or support issues to the mailing list:
 
 I<bioperl-l@bioperl.org>
 
-rather than to the module maintainer directly. Many experienced and 
-reponsive experts will be able look at the problem and quickly 
-address it. Please include a thorough description of the problem 
+rather than to the module maintainer directly. Many experienced and
+reponsive experts will be able look at the problem and quickly
+address it. Please include a thorough description of the problem
 with code and data examples if at all possible.
 
 =head2 Reporting Bugs
@@ -76,7 +76,7 @@ Bug reports can be submitted via the web.
 
   https://github.com/bioperl/bioperl-live/issues
 
-=head1 AUTHOR 
+=head1 AUTHOR
 
 Email cjfields at bioperl dot org
 

Bio/DB/Registry.pm

@@ -21,33 +21,33 @@ Bio::DB::Registry - Access to the Open Bio Database Access registry scheme
 =head1 DESCRIPTION
 
 This module provides access to the Open Bio Database Access (OBDA)
-scheme, which provides a single cross-language and cross-platform 
-specification of how to get to databases. These databases may be 
+scheme, which provides a single cross-language and cross-platform
+specification of how to get to databases. These databases may be
 accessible through the Web, they may be BioSQL databases, or
 they may be local, indexed flatfile databases.
 
-If the user or system administrator has not installed the default init 
-file, seqdatabase.ini, in /etc/bioinformatics or ${HOME}/.bioinformatics 
-then creating the first Registry object copies the default settings from 
-the www.open-bio.org. The Registry object will attempt to store these 
+If the user or system administrator has not installed the default init
+file, seqdatabase.ini, in /etc/bioinformatics or ${HOME}/.bioinformatics
+then creating the first Registry object copies the default settings from
+the www.open-bio.org. The Registry object will attempt to store these
 settings in a new file, ${HOME}/.bioinformatics/seqdatabase.ini.
 
-Users can specify one or more custom locations for the init file by 
-setting $OBDA_SEARCH_PATH to those directories, where multiple 
+Users can specify one or more custom locations for the init file by
+setting $OBDA_SEARCH_PATH to those directories, where multiple
 directories should be separated by ';'.
 
 Please see the OBDA Access HOWTO for more information
-(L<http://bioperl.open-bio.org/wiki/HOWTO:OBDA>).
+(L<http://bioperl.org/howtos/OBDA_HOWTO.html>).
 
-=head2 Support 
+=head2 Support
 
 Please direct usage questions or support issues to the mailing list:
 
 I<bioperl-l@bioperl.org>
 
-rather than to the module maintainer directly. Many experienced and 
-reponsive experts will be able look at the problem and quickly 
-address it. Please include a thorough description of the problem 
+rather than to the module maintainer directly. Many experienced and
+reponsive experts will be able look at the problem and quickly
+address it. Please include a thorough description of the problem
 with code and data examples if at all possible.
 
 =head2 Reporting Bugs
@@ -70,7 +70,7 @@ methods. Internal methods are usually preceded with a _
 package Bio::DB::Registry;
 
 use vars qw($OBDA_SPEC_VERSION $OBDA_SEARCH_PATH
-			   $HOME $PRIVATE_DIR $PUBLIC_DIR $REGISTRY 
+			   $HOME $PRIVATE_DIR $PUBLIC_DIR $REGISTRY
 			   $FALLBACK_REGISTRY);
 use strict;
 
@@ -174,7 +174,7 @@ sub _load_registry {
       } else {
 			eval {
 				my $randi = $class->new_from_registry( %{$hash->{$db}} );
-				$self->{'_dbs'}->{$db}->add_database($randi); 
+				$self->{'_dbs'}->{$db}->add_database($randi);
 			};
 			if ($@) {
 				$self->warn("Couldn't call new_from_registry() on [$class]\n$@");
@@ -246,7 +246,7 @@ sub _get_ini_files {
 			push @ini_files,$file;
       }
    }
-   push @ini_files,"$HOME/$PRIVATE_DIR/$REGISTRY" 
+   push @ini_files,"$HOME/$PRIVATE_DIR/$REGISTRY"
      if ( $HOME && -e "$HOME/$PRIVATE_DIR/$REGISTRY" );
    push @ini_files, "$PUBLIC_DIR/$REGISTRY"
      if ( -e "$PUBLIC_DIR/$REGISTRY" );
@@ -267,11 +267,11 @@ sub _make_private_registry {
 	my $self = shift;
    my @ini_file;
 
-	my $nor_in = $OBDA_SEARCH_PATH ? 
-	  "nor in directory specified by\n$OBDA_SEARCH_PATH" : 
+	my $nor_in = $OBDA_SEARCH_PATH ?
+	  "nor in directory specified by\n$OBDA_SEARCH_PATH" :
 	  "and environment variable OBDA_SEARCH_PATH wasn't set";
 
-	$self->warn("No $REGISTRY file found in $HOME/$PRIVATE_DIR/\n" . 
+	$self->warn("No $REGISTRY file found in $HOME/$PRIVATE_DIR/\n" .
 					"nor in $PUBLIC_DIR $nor_in.\n" .
 					"Using web to get registry from\n$FALLBACK_REGISTRY");
 

Bio/ParameterBaseI.pm

@@ -1,7 +1,7 @@
 #
 # BioPerl module for Bio::ParameterBaseI
 #
-# Please direct questions and support issues to <bioperl-l@bioperl.org> 
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
 #
 # Cared for by Chris Fields <cjfields at bioperl dot org>
 #
@@ -87,7 +87,7 @@ Implementing classes use the following ways to set parameters:
 2) Pass the parameters as a hash or array to set_parameters(), which sets the
 parameters listed in the hash but leaves all others as is.
 
-  $pobj->set_parameters(-retmax => 100, -retstart => 20); 
+  $pobj->set_parameters(-retmax => 100, -retstart => 20);
 
 3) Pass the parameters as a hash or array to reset_parameters(), which sets the
 parameters listed in the hash and resets everything else.
@@ -107,18 +107,18 @@ ParameterBaseI object so that any object with a Bio::ParameterBaseI can decide
 whether to submit a new request or return cached data. State changes are
 revealed by the returned values of the parameters_changed() method, which is a
 simple boolean set to TRUE when the object is first instantiated or parameters
-have changed. 
+have changed.
 
 When retrieving anything using the implementation-specific to_* methods (such as
 to_query, to_string, to_uri, to_request, etc), the ParameterBaseI object state
 is set to FALSE to indicate the data has been accessed and indicate reaccessing
 will retrieve the same value. The observing object can then independently decide
-whether to rerun the cached query or return a previously cached result. 
+whether to rerun the cached query or return a previously cached result.
 
 One can also use indiviual getter/setters to retrieve single parameter values as
 well as use parameter_hash() to retrieve all of the parameters in one go as a
 hash. To check which parameters are available use available_parameters().  Args
-passed to 
+passed to
 
 =head1 FEEDBACK
 
@@ -131,17 +131,17 @@ of the Bioperl mailing lists. Your participation
 is much appreciated.
 
   bioperl-l@lists.open-bio.org               - General discussion
-  http://www.bioperl.org/wiki/Mailing_lists  - About the mailing lists
+  http://bioperl.org/Support.html  - About the mailing lists
 
-=head2 Support 
+=head2 Support
 
 Please direct usage questions or support issues to the mailing list:
 
 I<bioperl-l@bioperl.org>
 
-rather than to the module maintainer directly. Many experienced and 
-reponsive experts will be able look at the problem and quickly 
-address it. Please include a thorough description of the problem 
+rather than to the module maintainer directly. Many experienced and
+reponsive experts will be able look at the problem and quickly
+address it. Please include a thorough description of the problem
 with code and data examples if at all possible.
 
 =head2 Reporting Bugs
@@ -178,7 +178,7 @@ use base qw(Bio::Root::RootI);
  Usage   : $pobj->set_parameters(%params);
  Function: sets the parameters listed in the hash or array
  Returns : None
- Args    : [optional] hash or array of parameter/values.  
+ Args    : [optional] hash or array of parameter/values.
 
 =cut